[PyMOL] ANNOUNCE: apropos command to lookup commands matching a keyword.
Hi there,
I have written a little utility called apropos[1] (after a unix command of the
same name) to help in locating commands that might do something
you want done. It is like the grepset[2] command except this one looks
up commands instead of settings.
[1] http://www.pymolwiki.org/index.php/Apropos
[2] http://www.pymolwiki.org/index.php/Grepset
Comments are welcome.
Have fun,
Zac
#
# apropos.py
# Author: Ezequiel Panepucci
# Date: 2006-07-20
#
from pymol import cmd
import re
def apropos(regexp=''):
'''
DESCRIPTION
apropos searches through the documentation of all currently
defined commands and lists those commands for which the keyword
is either contained in the documentation or matches the command
name itself.
If an appropriate DESCRIPTION section is provided in the documentation
of the command, the first 80 characters are listed as a summary.
USAGE
apropos [keyword or regexp]
EXAMPLE
apropos fit
###EXACT MATCH FOR: fit == try 'help fit' at the prompt.
###The following commands are NOT documented.
vdw_fit
###The following commands are documented. 'help command'
fit : fit superimposes the model in the first selection on to the model
intra_fit : intra_fit fits all states of an object to an atom selection
rms : rms computes a RMS fit between two atom selections, but does not
pair_fit : pair_fit fits a set of atom pairs between two models. Each atom
intra_rms_cur : intra_rms_cur calculates rms values for all states of an object
commands : Ooopsie, no DESCRIPTION found for this command!!!
zoom : zoom scales and translates the window and the origin to cover the
intra_rms : intra_rms calculates rms fit values for all states of an object
align : align performs a sequence alignment followed by a structural
rms_cur : rms_cur computes the RMS difference between two atom
fitting : fitting allows the superpositioning of object1 onto object2 using
SEE ALSO
grepset(www.pymolwiki.org), Python re module
'''
cmd.set(text,1,quiet=1)
count=0
docre = re.compile(regexp, re.MULTILINE | re.IGNORECASE)
cmdre = re.compile(regexp, re.IGNORECASE)
matches_with_help = []
matches_without_help = []
maxcclen=0
for cc in cmd.keyword:
if cc == regexp:
print '\n###EXACT MATCH FOR: %s == try \'help %s\' at the prompt.' % (cc,cc)
doc = cmd.keyword[cc][0].__doc__
if doc == None:
if re.search(regexp, cc, re.IGNORECASE):
count += 1
matches_without_help.append(cc)
continue
if re.search(regexp, doc, re.MULTILINE | re.IGNORECASE):
count += 1
if len(cc) maxcclen:
maxcclen = len(cc)
docmatches = re.match(r^\s+DESCRIPTION\s+(.{0,80})\S*, doc, re.IGNORECASE)
if docmatches == None:
desc = ' Ooopsie, no DESCRIPTION found for this command!!! '
else:
desc = docmatches.groups()[0]
matches_with_help.append( (cc, desc ) )
if len(matches_without_help) 0:
fmt = '%' + str(maxcclen) + 's' # get the width of the lenghtiest command in a format
print '\n###The following commands are NOT documented.\n'
for cc in matches_without_help:
print fmt % (cc)
if len(matches_with_help) 0:
fmt = '%' + str(maxcclen) + 's : %s' # get the width of the lenghtiest command in a format
print '\n###The following commands are documented. \'help command\' \n'
for (cc,desc) in matches_with_help:
print fmt % (cc,desc)
cmd.extend('apropos',apropos)
[PyMOL] ANNOUNCE: apropos command to lookup commands matching a keyword.
Hi there,
I have written a little utility called apropos[1] (after a unix command of the
same name) to help in locating commands that might do something
you want done. It is like the grepset[2] command except this one looks
up commands instead of settings.
[1] http://www.pymolwiki.org/index.php/Apropos
[2] http://www.pymolwiki.org/index.php/Grepset
Comments are welcome.
Have fun,
Zac
#
# apropos.py
# Author: Ezequiel Panepucci
# Date: 2006-07-20
#
from pymol import cmd
import re
def apropos(regexp=''):
'''
DESCRIPTION
apropos searches through the documentation of all currently
defined commands and lists those commands for which the keyword
is either contained in the documentation or matches the command
name itself.
If an appropriate DESCRIPTION section is provided in the documentation
of the command, the first 80 characters are listed as a summary.
USAGE
apropos [keyword or regexp]
EXAMPLE
apropos fit
###EXACT MATCH FOR: fit == try 'help fit' at the prompt.
###The following commands are NOT documented.
vdw_fit
###The following commands are documented. 'help command'
fit : fit superimposes the model in the first selection on to the model
intra_fit : intra_fit fits all states of an object to an atom selection
rms : rms computes a RMS fit between two atom selections, but does not
pair_fit : pair_fit fits a set of atom pairs between two models. Each atom
intra_rms_cur : intra_rms_cur calculates rms values for all states of an object
commands : Ooopsie, no DESCRIPTION found for this command!!!
zoom : zoom scales and translates the window and the origin to cover the
intra_rms : intra_rms calculates rms fit values for all states of an object
align : align performs a sequence alignment followed by a structural
rms_cur : rms_cur computes the RMS difference between two atom
fitting : fitting allows the superpositioning of object1 onto object2 using
SEE ALSO
grepset(www.pymolwiki.org), Python re module
'''
cmd.set(text,1,quiet=1)
count=0
docre = re.compile(regexp, re.MULTILINE | re.IGNORECASE)
cmdre = re.compile(regexp, re.IGNORECASE)
matches_with_help = []
matches_without_help = []
maxcclen=0
for cc in cmd.keyword:
if cc == regexp:
print '\n###EXACT MATCH FOR: %s == try \'help %s\' at the prompt.' % (cc,cc)
doc = cmd.keyword[cc][0].__doc__
if doc == None:
if re.search(regexp, cc, re.IGNORECASE):
count += 1
matches_without_help.append(cc)
continue
if re.search(regexp, doc, re.MULTILINE | re.IGNORECASE):
count += 1
if len(cc) maxcclen:
maxcclen = len(cc)
docmatches = re.match(r^\s+DESCRIPTION\s+(.{0,80})\S*, doc, re.IGNORECASE)
if docmatches == None:
desc = ' Ooopsie, no DESCRIPTION found for this command!!! '
else:
desc = docmatches.groups()[0]
matches_with_help.append( (cc, desc ) )
if len(matches_without_help) 0:
fmt = '%' + str(maxcclen) + 's' # get the width of the lenghtiest command in a format
print '\n###The following commands are NOT documented.\n'
for cc in matches_without_help:
print fmt % (cc)
if len(matches_with_help) 0:
fmt = '%' + str(maxcclen) + 's : %s' # get the width of the lenghtiest command in a format
print '\n###The following commands are documented. \'help command\' \n'
for (cc,desc) in matches_with_help:
print fmt % (cc,desc)
cmd.extend('apropos',apropos)
